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high-throughput phenotyping

Developing and bringing new agricultural products to market can be costly and time consuming for industry. Nufarm Limited recently sought the technology and expertise of the Australian Plant Phenomics Facility (APPF) to provide independent testing on potential new foliar sprays under development.

“The full service approach at the APPF, from the technology to the specialist staff, really appealed to us”, said Chad Sayer from Nufarm’s Product Strategy Group.

“The non-destructive, high-throughput phenotyping technology at the APPF gave us the ability to gain insights into our products under development that we could not achieve anywhere else. Their highly skilled, specialist team helped us design our experiments and provided invaluable advice throughout the project, right through to the data analysis.

“This has been exciting for us. Our pilot project delivered such promising results, we already have a large project underway”.

“We have a bespoke approach, working closely with our customers to design their experiments to deliver the best results”, said Dr Bettina Berger, Scientific Director at the Adelaide node of the APPF.

Dr Berger and her colleagues provide consultation on all projects carried out at the Adelaide node, supporting the development of the initial design and execution of the research. The specialist horticultural team set up the experiments and manage them through to completion. Customers can make use of online monitoring and access of projects throughout the experiment stage via Zegami (‘live processing’ which allows result checking on a day-to-day basis). On completion of experiments image analysis and data analysis are handled by our skilled engineering, software and statistics team. The research team then provide consultation on results and further follow-up as required.

Plants in a Smarthouse at the Adelaide node of the APPF undergo daily image analysis throughout the experiment

The APPF is available to all publicly or commercially funded researchers. For further information or to discuss how we can support your research, please visit theAPPF website for contact details. For more information about this project, contact Dr Berger.

Nufarm Limited is an Australian company. It is one of the world’s leading crop protection and specialist seeds companies, producing products to help farmers protect their crops against damage caused by weeds, pests and disease. With operations based in Australia, New Zealand, Asia, Europe and the Americas, Nufarm sells products in more than 100 countries around the world. Find out more about Nufarmhere.

Zegami is a web application which allows users to filter, sort and chart data from experiments undertaken in the Smarthouses at the APPF Adelaide node, with the unique feature of being able to group that data with the corresponding images. To get a real feel for the application, we highly recommend you watch the video. Further reading here.

Resource Recovery Australia together with CSIRO, Cape York Partnership, Balkanu and Kalan Enterprises are developing new income streams for Cape York’s Aboriginal communities by producing organic soil-conditioners from an unlikely source, feral pigs, which cause vast environmental damage to native ecosystems.

A pilot project at the Australian Plant Phenomics Facility’s (APPF) Adelaide node, tested the effect of the ‘Feraliser’ at different concentrations on tomato growth.

“The data collected using the high-throughput phenotyping Smarthouse at the APPF provided valuable insights into the effectiveness of our product. We now know Feraliser performs just as well as the leading organic soil-conditioners currently on the market,” said Emmaline Froggatt from Resource Recovery Australia.

“Feraliser is very much at the start-up phase of development so costs are a big issue for us. The Australian Plant Phenomics Facility provided the information we needed without the expense of a full field trial.”

A recent study has collected phenotypic data of chickpea (Cicer arietinum L.) which can now be linked with the genotypic data of these lines. This will enable genome-wide association mapping with the aim of identifying loci that underlie salinity tolerance – an important step in developing salt tolerant chickpeas.

In this study, Judith Atieno and co-authors utilised image-based phenotyping at the Australian Plant Phenomics Facility to study genetic variation in chickpea for salinity tolerance in 245 diverse accessions (a diversity collection, known as the Chickpea Reference Set).

Chickpea is an important legume crop, used as a highly nutritious food source and grown in rotation with cereal crops to fix nitrogen in the soil or to act as a disease break. However, despite its sensitivity to salt, chickpea is generally grown in semi-arid regions which can be prone to soil salinity. This results in an estimated global annual chickpea yield loss of between 8–10%.

Salinity tolerance phenotyping in a Smarthouse at the Australian Plant Phenomics Facility’s Adelaide node at the Waite Research Precinct – Plants were imaged at 28 DAS for 3 consecutive days prior to 40 mM NaCl application in two increments over 2 days. Plants were daily imaged until 56 DAS. Right pane shows 6-week-old chickpeas on conveyor belts leaving the imaging hall proceeding to an automatic weighing and watering station.

The study found, on average, salinity reduced plant growth rate (obtained from tracking leaf expansion through time) by 20%, plant height by 15% and shoot biomass by 28%. Additionally, salinity induced pod abortion and inhibited pod filling, which consequently reduced seed number and seed yield by 16% and 32%, respectively. Importantly, moderate to strong correlation was observed for different traits measured between glasshouse and two field sites indicating that the glasshouse assays are relevant to field performance. Using image-based phenotyping, we measured plant growth rate under salinity and subsequently elucidated the role of shoot ion independent stress (resulting from hydraulic resistance and osmotic stress) in chickpea. Broad genetic variation for salinity tolerance was observed in the diversity panel with seed number being the major determinant for salinity tolerance measured as yield. The study proposes seed number as a selection trait in breeding salt tolerant chickpea cultivars.

Genotypic variation for salinity tolerance in the Chickpea Reference Set. Varying levels of salinity tolerance exhibited by different chickpea genotypes. Exposure of sensitive genotypes to 40 mM NaCl caused severe stunted growth, leaf damage, and led to less number of reproductive sites (flowers and pods) compared to moderately tolerant and tolerant genotypes.

The rapid development of new, high-resolution and high-throughput phenotyping technologies in plant science has provided the opportunity to more deeply explore genetic variation for salinity tolerance in crop species and identify traits that are potentially novel and relevant to yield improvement. The Australian Plant Phenomics Facility provides state-of-the-art phenotyping and analytical tools and expertise in controlled environments and in the field to help academic and commercial plant scientists understand and relate the performance of plants to their genetic make-up. A dedicated cross-disciplinary team of experts provides consultation on project design and high quality support.

To read the full paper in Scientific Reports,“Exploring genetic variation for salinity tolerance in chickpea using image-based phenotyping” (doi:10.1038/s41598-017-01211-7), click here.

To find out more about the Australian Plant Phenomics Facility and how we can support your researchclick here.

In a recent paper, researchers have developed a methodology suitable for analyzing the growth curves of a large number of plants from multiple families. The corrected curves accurately account for the spatial and temporal variations among plants that are inherent to high-throughput experiments.

An example of curve registration. a The salinity sensitivity (SS) curves of the 16 functions from an arbitrary family, b SS curves after the curve registration, and c the corresponding time-warping functions. The salinity sensitivity on the y-axis of a and b refers to the derivative of the relative decrease in plant biomass

Advanced high-throughput technologies and equipment allow the collection of large and reliable data sets related to plant growth. These data sets allow us to explore salt tolerance in plants with sophisticated statistical tools.

As agricultural soils become more saline, analysis of salinity tolerance in plants is necessary for our understanding of plant growth and crop productivity under saline conditions. Generally, high salinity has a negative effect on plant growth, causing decreases in productivity. The response of plants to soil salinity is dynamic, therefore requiring the analysis of growth over time to identify lines with beneficial traits.

In this paper the researchers, led by KAUST and including Dr Bettina Berger and Dr Chris Brien from the Australian Plant Phenomics Facility (APPF), use a functional data analysis approach to study the effects of salinity on growth patterns of barley grown in the high-throughput phenotyping platform at the APPF. The method presented is suitable to reduce the noise in large-scale data sets and thereby increases the precision with which salinity tolerance can be measured.

Statistics prove the smart way to deal with variation in your controlled environment greenhouse.

Plant phenomics allows the measurement of plant growth with unprecedented precision. As a result, the question of how to account for the influence of environmental variation across the greenhouse has gained attention.

Controlled environment greenhouses offer plant scientists the ability to better understand the genetic elements of specific plant traits by reducing the environmental variances in the interaction between genetics and environment.

But controlled environments aren’t as controlled as they seem – variation does exist. For example, some days are cloudy, some are not. The sun, as it crosses the sky, casts shadows differently on plants, depending on their position within the greenhouse. In fact, a recent study by colleagues at INRA in Montpellier showed significant light gradients within a greenhouse and provided sophisticated tools for understanding how much light each plant receives.

One practice for dealing with variation has been to rearrange the position of the plants around the greenhouse during the experiment, however, there is a better way.

Rice plants growing in The Plant Accelerator® at the Australian Plant Phenomics Facility’s Adelaide node

The automated high-throughput phenotyping greenhouses at The Plant Accelerator® are controlled environment facilities which use sensor networks to identify and quantify environmental gradients (light, temperature, humidity) in the greenhouses. To further tackle environmental variation, Chris Brien, Senior Statistician at The Plant Accelerator®, led a study that showed good statistical design and analysis was key to accounting for the impact of environmental gradients on plant growth. It was argued that rearranging the plants during the experiment makes it impossible to adjust for the effect of gradients and should be avoided.

The study involved a two-phase wheat experiment involving four tactics in a conventional greenhouse and a controlled environment greenhouse at The Plant Accelerator® to investigate these issues by measuring the effect of the variation on plant growth.

To discuss the benefits of good statistical design contact Chris Brien.

To access The Plant Accelerator® for your research: The Plant Accelerator® at the Australian Plant Phenomics Facility (APPF) is available to all publicly or commercially funded researchers. We have a full team of specialists including statisticians, horticulturalists and plant scientists who can provide expert advice to you when preparing your research plans.